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(-) Description

Title :  AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-INDOLEBUTYRIC ACID
 
Authors :  A. Okamoto, K. Hirotsu, H. Kagamiyama
Date :  06 Aug 98  (Deposition) - 02 Feb 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Okamoto, S. Ishii, K. Hirotsu, H. Kagamiyama
The Active Site Of Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase Has Contrary Properties: Flexibility And Rigidity.
Biochemistry V. 38 1176 1999
PubMed-ID: 9930977  |  Reference-DOI: 10.1021/BI981921D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AROMATIC AMINO ACID AMINOTRANSFERASE
    ChainsA, B
    EC Number2.6.1.57
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC118
    Expression System StrainTY103
    Expression System Taxid562
    Organism ScientificPARACOCCUS DENITRIFICANS
    Organism Taxid266
    StrainIFO 12442
    SynonymAROAT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
13IB1Ligand/Ion3-INDOLEBUTYRIC ACID
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:107 , GLY A:108 , THR A:109 , TRP A:140 , ASN A:194 , ASP A:222 , ALA A:224 , TYR A:225 , SER A:255 , SER A:257 , LYS A:258 , ARG A:266 , TYR B:70BINDING SITE FOR RESIDUE PLP A 413
2AC2SOFTWARETYR A:70 , GLY B:108 , THR B:109 , TRP B:140 , ASN B:194 , ASP B:222 , ALA B:224 , TYR B:225 , SER B:255 , SER B:257 , LYS B:258 , ARG B:266 , 3IB B:414BINDING SITE FOR RESIDUE PLP B 413
3AC3SOFTWARETYR A:70 , SER A:296 , ASP B:15 , ILE B:17 , GLY B:38 , TRP B:140 , ASN B:142 , ASN B:194 , LYS B:258 , ARG B:386 , PLP B:413BINDING SITE FOR RESIDUE 3IB B 414

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AY6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asp A:137 -Pro A:138
2Asn A:194 -Pro A:195
3Asp B:137 -Pro B:138
4Asn B:194 -Pro B:195

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AY6)

(-) Exons   (0, 0)

(no "Exon" information available for 2AY6)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:394
 aligned with TYRB_PARDE | P95468 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390    
           TYRB_PARDE     1 MLGNLKPQAPDKILALMGEFRADPRQGKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETETTKTYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRVFVSDPTWPNHVSIMNFMGLPVQTYRYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHNPTGANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAASCSKNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPELRADWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKEEFGIYMVGDSRINIAGLNDNTIPILARAIIEVGV 394
               SCOP domains d2ay6a_ A: Aromatic aminoacid aminotransferase, AroAT                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------2ay6A01 A:15-48,A:328-408         2ay6A02 A:49-327 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                        2ay6A01 A:15-48,A:328-408 Aspartate Aminotransferase, domain 1                   - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhh......ee................hhhhhhhhhhhhh............hhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhh...eeeee..........hhhhhhhh.......eeeee............hhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhh...eeeeee...........eeeeeee...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhh....eee....hhhhhhhhhhh.ee.....eee.......hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ay6 A   5 MLGNLKPQAPDKILALMGEFRADPRQGKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETETTKTYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRVFVSDPTWPNHVSIMNFMGLPVQTYRYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHNPTGANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAASCSKNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPELRADWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKEEFGIYMVGDSRINIAGLNDNTIPILARAIIEVGV 409
                                    14        24        34        44        54        64|       75        85     || 98       108       118       133       143       154       164       174       184       194       204       214       224      |235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405    
                                                                                      64|                       91|                            126||                152|                                                                          231|                                                                                                                                                                                
                                                                                       66                        95                             129|                 154                                                                           233                                                                                                                                                                                
                                                                                                                                                 133                                                                                                                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:388
 aligned with TYRB_PARDE | P95468 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:394
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390    
           TYRB_PARDE     1 MLGNLKPQAPDKILALMGEFRADPRQGKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETETTKTYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRVFVSDPTWPNHVSIMNFMGLPVQTYRYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHNPTGANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAASCSKNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPELRADWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKEEFGIYMVGDSRINIAGLNDNTIPILARAIIEVGV 394
               SCOP domains d2ay6b_ B: Aromatic       aminoacid aminotransferase, AroAT                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------2ay6B01 B:      15-48,B:328-408   2ay6B02 B:49-327 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                        2ay6B01 B:15-48,B:328-408 Aspartate Aminotransferase, domain 1                   - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhh.------..ee................hhhhhhhhhhhhh............hhhhhhhhhhhh........eeeeee.hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhh...eeeee.ee....ee.hhhhhhhh.......eeeee............hhhhhhhhhhhhhh..eeeeee........hhhh.hhhhhhhhh...eeeeee............eeeeee...hhhhhhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhh...........hhhhhhhhh...ee...............hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ay6 B   5 MLGNLKPQAPDKILALMGEF------GKIDLGVGVYKDATGHTPIMRAVHAAEQRMLETETTKTYAGLSGEPEFQKAMGELILGDGLKSETTATLATVGGTGALRQALELARMANPDLRVFVSDPTWPNHVSIMNFMGLPVQTYRYFDAETRGVDFEGMKADLAAAKKGDMVLLHGCCHNPTGANLTLDQWAEIASILEKTGALPLIDLAYQGFGDGLEEDAAGTRLIASRIPEVLIAASCSKNFGIYRERTGCLLALCADAATRELAQGAMAFLNRQTYSFPPFHGAKIVSTVLTTPELRADWMAELEAVRSGMLRLREQLAGELRDLSGSDRFGFVAEHRGMFSRLGATPEQVKRIKEEFGIYMVGDSRINIAGLNDNTIPILARAIIEVGV 409
                                    14        24      | 34        44        54        64|       75        85     || 98       108       118       133       143       154       164       174       184       194       204       214       224      |235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405    
                                              24     31                               64|                       91|                            126||                152|                                                                          231|                                                                                                                                                                                
                                                                                       66                        95                             129|                 154                                                                           233                                                                                                                                                                                
                                                                                                                                                 133                                                                                                                                                                                                                                                                                  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AY6)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TYRB_PARDE | P95468)
molecular function
    GO:0080130    L-phenylalanine:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: L-phenylalanine + 2-oxoglutarate = phenylpyruvate + L-glutamate.
    GO:0008793    aromatic-amino-acid:2-oxoglutarate aminotransferase activity    Catalysis of the reaction: an aromatic amino acid + 2-oxoglutarate = an aromatic oxo acid + L-glutamate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TYRB_PARDE | P954681ay4 1ay5 1ay8 2ay1 2ay2 2ay3 2ay4 2ay5 2ay7 2ay8 2ay9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2AY6)